GeneNetworkBuilder: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")
AuthorJianhong Ou , Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu
Bioconductor views GraphAndNetwork Microarray Sequencing
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.16.0

View on Bioconductor

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/GeneNetworkBuilder.R R/applications.R
build
build/vignette.rds
data
data/ce.IDsMap.rda
data/ce.interactionmap.rda
data/ce.mapIDs.rda
data/ce.miRNA.map.rda
data/datalist
data/example.data.rda
data/hs.IDsMap.rda
data/hs.interactionmap.rda
data/hs.mapIDs.rda
data/hs.miRNA.map.rda
inst
inst/doc
inst/doc/GeneNetworkBuilder.R
inst/doc/GeneNetworkBuilder.Rnw
inst/doc/GeneNetworkBuilder.pdf
inst/unitTests
inst/unitTests/test_geneNetworkBuilder.R
man
man/buildNetwork.Rd man/ce.IDsMap.Rd man/ce.interactionmap.Rd man/ce.mapIDs.Rd man/ce.miRNA.map.Rd man/convertID.Rd man/example.data.Rd man/filterNetwork.Rd man/hs.IDsMap.Rd man/hs.interactionmap.Rd man/hs.mapIDs.Rd man/hs.miRNA.map.Rd man/polishNetwork.Rd man/uniqueExprsData.Rd
src
src/Makevars
src/Makevars.win
src/geneTree.cpp
src/geneTree.h
src/nodefilter.cpp
tests
tests/runTests.R
vignettes
vignettes/GeneNetworkBuilder.Rnw
vignettes/hs_sample_rcytoscape.eps
vignettes/hs_sample_rcytoscape.pdf
vignettes/workflow.eps
vignettes/workflow.pdf

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.